One of the application areas for magnetic nanoparticles (MNPs) is in cell labeling and magnetic separation. This process involves tagging MNPs onto desired cells and then separating them from unwanted entities using a sensor which retains them when an external magnetic field is applied. The number of cells retained on the sensor can be determined by measuring the total signal change and dividing it by the change in signal from a single MNP. Accurate quantification requires that the MNPs be uniform in shape, size, composition, and free from clustering. The Transmission Electron Microscope (TEM) is an appropriate characterization tool owing to its sub-nanometer resolution. Using this technique, four different types of iron oxide nanoparticles were examined and their phases were determined. Commercially available MNPs are found to be “beads” comprising multiple iron-oxide cores encapsulated by polymer shells. The cores are log-normally distributed in size with large standard deviations. The beads also have the tendency to form clusters. On the other hand, MNPs synthesized by our collaborators are single-core iron oxide nanoparticles which demonstrate good uniformity in size, good crystalline nature and are free of clustering. The latter are expected to be superior candidates for the required application.